What did you do to your trains today?

That's curious. I've seen TrackMaster 2 track painted for more realism before, but doing it with TM1 seems uncommon to me. In terms of adding more shades to the ballast, it might be effective to use cotton wool dipped in some of each colour to spread them with light presses against the "gravel" (same method for the sleepers). I hope there might be a good way to ensure paint wouldn't rub off where the rolling stock runs. Alternatively, you could try using a black marker and remove it with alcohol (also on cotton wool) to see if it helps. Looking forward to the improvements.